Hi Chih-Hao Lien,

You are right, CONN will disregard specific ROIs if they fall entirely outside of the brain for some subject(s), so I imagine that could perhaps be causing the missing ROIs in your case?. 

Best

Alfonso

Originally posted by Chihhao Lien:

Hi Alfonso,

I checked my problem again, and I'd like to provide more details.
In names variable of resultsROI*.mat, I found only 140 ROIs, which should be 142 ROIs from the neuromorphometrics atlas while inputting the atlas file you provided in the CONN toolbox.

Two ROIs, including the Left Inferior Lateral Ventricle and Left Optic Chiasm, are not on the list now.

I also checked Setup -> ROIs -> NeuroMorphometrics Atlas

It looks like most ROIs are located in the proper locations.

I can find the Right Inferior Lateral Ventricle and Right Optic Chiasm, but not the contralateral ROIs.

I don't need these 2 ROIs, but I'm wondering if the CONN toolbox ignores tiny ROIs or ROIs outside the brain silhouette. 

Best regards,

Chih-Hao Lien